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<div class="moz-cite-prefix">Dear Pierre,</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">thank you for your email and for the
list of spacegroup vs. symop mismatch, and sorry for a delay with
the answer.</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">I've looked into the log and blow are
my comments, based on my interpretation of this log.</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">First of all, you are absolutely write
to use symmetry operations provided in the CIF if these are
available and interpretable. This is our standard procedure and
recommendation to COD users. Symmetry operations are the most
versatile way to describe symmetry relations in a computer- and
human-readable form, so that can always be used. In contrast,
Hermann-Mauguin and even Hall symbols can give humans a symbolic
identification of the space group, but they lack a standard way to
express all varieties of settings, cell choices and origins used
nowadays by crystallographers.</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">The Hermann-Mauguin and Hall symbols <i>can</i>
be adapted to express multiple (all?) non-standard settings and
origins; for this, however, a Change of Basis matrix must be used,
or at least Shift of Origin which might be sufficient in some
cases. Unfortunately, there is no standard way to encode these
elements (I am seriously considering writing up a standardisation
proposal to IUCr...), but the current use in published literature
(even in the Tables!) attests the following uses:</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">
<div class="moz-cite-prefix"> -- Parse the Change of Basis (CoB)
operator strings in the form<br>
-- "(a-b,a+b,c)" or "(x-y,x+y,z)" and return a matrix that
encodes<br>
-- this operator. The CoB is described in [1,2].<br>
--<br>
-- The 'abc' for is a transpose inverse of the 'xyz' form.<br>
</div>
<div class="moz-cite-prefix"><br>
</div>
</div>
<div class="moz-cite-prefix">The use cases and brief mention of
these conventions can be found in IUCr sources [1,3] or on the Web
by the same authors [2].</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">We in the COD adopted these
conventions, and I wrote a small parser for the space group symbol
interpretation [4] to make these conventions explicit. The code is
in Ada which, although not in the top 5 popularity list :), is
very readable, standard and stable. To see how we interpret the
extended H-M and Hall space group symbol strings, you may want to
look into the Change_of_Basis Ada package [5].</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">I would thus like to ask you a question
as to what you mean by saying that "list of symmetries is
obviously wrong or contradicts the Bravais symbol in the group
name"?</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">So, for example, in the COD 1001841
entry which is mentioned first in your log, the space group symbol
derived form the symmetry operations is 'P 2yb (-1/2*x+z,1/2*x,y)'
(Hall), or 'P 1 21 1 (c,2*a+c,b)' (H-M). Both symbols yield
identical symmetry operations when decoded by my program [4], and
they coincide with the symmetry operation lists given in the COD
entry. The space group for this crystal is ITC No. 4, H-M symbol
'P 21'. However, for whatever reason authors chose to represent
the structure in a C-centered cell (probably to compare with a
similar C2 structure or something like that). They identified the
space group as 'C1121', which is of course a non-standard symbol
and cell choice for this space group, but that is what the authors
reported.</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">When I calculate the crystal
composition using the symmetry operations and the atom list that
the authors provided, I get the summary formula "La3 O8 Re",
exactly like authors have reported. Thus, I conclude that this
structure is reported the way it was intended by the authors.</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">To interpret the space group symbols,
it is not enough to take just the Table symmetries for P1211
(which you list in your log); you need to analyse the
change-of-basis as well, so to interpret the whole string 'P 1 21
1 (c,2*a+c,b)' given in the file; this will yield four symmetry
operations, not two.</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">It seems that many of your log entries
are of similar kind, representing non-standard settings and cell
choices.</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">In some cases, like for COD 1553126,
you report the duplicated symmetry operations, while in fact they
are not: in this entry, the symmetry operations are present under
different data names ("_space_group_symop_operation_xyz" and
"_symmetry_equiv_pos_as_xyz"), one of the old and another new.
This is not a bug, all data names are permitted in the CIF, as
long as the symmetry operation lists are equivalent. Please make
sure that you software correctly chooses one set of symmetry
operations or another (we suggest using newer CIF name if it
exists, and falling back to the old one if the new one is
missing).</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">There are other cases where the same
data names report different symmetry operations sets, like in COD
1564490. This is indeed wrong, thanks for spotting such cases! We
will have to look into them individually.</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">My plans are to update our the space
group symbol determination software and to assign space group
names with the change-of-basis operators to all remaining COD
entries that do not have these designations. Also, we will check
that the "_space_group_symop_operation_xyz" and
"_symmetry_equiv_pos_as_xyz", if they exists, always report
correct symmetry operations.</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">What you can do on your side is to make
sure that your program pick only one data item, "_space_group_symop_operation_xyz"
or "_symmetry_equiv_pos_as_xyz", the one that has complete
symmetry operation list (i.e. contains unity operation 'x,y,z' and
the specified symops form a group), and that the program either
interprets the change-of-basis operators or ignore space group
symbols that have them.</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">HTH,</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">Saulius<br>
</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">Refs.:</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">[1] Zwart, P. H.; Grosse-Kunstleve, R.
W.; Lebedev, A. A.;<br>
Murshudov, G. N. & Adams, P. D. (2007) Surprises and pitfalls<br>
arising from (pseudo)symmetry. Acta Crystallographica Section D<br>
Biological Crystallography 64(1), 99-107. International Union<br>
of Crystallography (IUCr). DOI:<br>
<a class="moz-txt-link-freetext" href="https://doi.org/10.1107/s090744490705531x">https://doi.org/10.1107/s090744490705531x</a><br>
</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">[2] Sydney R. Hall, Ralf W.
Grosse-Kunstleve (1996) "Concise<br>
Space-Group Symbols". URL:<br>
<a class="moz-txt-link-freetext" href="https://cci.lbl.gov/sginfo/hall_symbols.html">https://cci.lbl.gov/sginfo/hall_symbols.html</a> [accessed:<br>
2022-06-14T15:24+03:00]<br>
<br>
[3] International Tables Volume B (2010), "Symmetry in<br>
reciprocal space". Section 1.4., Appendix A1.4.2. Space-group<br>
symbols for numeric and symbolic computations, URL:<br>
<a class="moz-txt-link-freetext" href="https://onlinelibrary.wiley.com/iucr/itc/B/">https://onlinelibrary.wiley.com/iucr/itc/B/</a> [accessed:<br>
2022-06-14T15:35+03:00]<br>
</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">[4] Gražulis, S. (2024)
decode-Hall-symbol [computer software].
<a class="moz-txt-link-freetext" href="https://github.com/sauliusg/decode-Hall-symbol">https://github.com/sauliusg/decode-Hall-symbol</a></div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">[5] Gražulis, S. (2024)
decode-Hall-symbol [computer software]. Ada package
'Change_Of_Basis'.
<a class="moz-txt-link-freetext" href="https://github.com/sauliusg/decode-Hall-symbol/blob/master/src/change_of_basis.ads">https://github.com/sauliusg/decode-Hall-symbol/blob/master/src/change_of_basis.ads</a>,
<a class="moz-txt-link-freetext" href="https://github.com/sauliusg/decode-Hall-symbol/blob/master/src/change_of_basis.adb">https://github.com/sauliusg/decode-Hall-symbol/blob/master/src/change_of_basis.adb</a><br>
</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">On 2025-09-02 11:03, Caussin, Pierre
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:FR0P281MB31006A8F5E93DCBAC75517B9EB06A@FR0P281MB3100.DEUP281.PROD.OUTLOOK.COM">
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<p class="MsoNormal"><span style="font-size:11.0pt">Hi there,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">I am working
for Bruker and trying to better streamline the use of the
COD in our search/match and semiquantitative software. One
of the goals is being able to compute the peak positions and
relative intensities and RIR of COD entries. We do this at
CuKA1 wavelength for all the entries that have a structure
and space group given (all entries except 1119 that have
either no atomic coordinates and/or blank or unknown space
group, which are currently ignored). This compilation is
done using the symmetries stored in the CIF file.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">To be able
to compute the selected entries at other wavelengths on the
fly, we need the space group symmetries, without keeping the
complete CIFs, which use over 26GB after ZIP compression. I
have written code to create a table [space group HM name]
=> [table of symmetries]. This works well, but I have
found 478 CIF files where the given HM name appears to
contradict the list of symmetries. I enclose the diagnostic
output of my program (plus my case-by-case comment ‘//’),
which can be summarized in two cases:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<ol style="margin-top:0in" start="1" type="1">
<li class="MsoListParagraph"
style="margin-left:0in;mso-list:l0 level1 lfo1"><span
style="font-size:11.0pt">The list of symmetries is
obviously wrong or contradicts the Bravais symbol in the
group name<o:p></o:p></span></li>
<li class="MsoListParagraph"
style="margin-left:0in;mso-list:l0 level1 lfo1"><span
style="font-size:11.0pt">The list of symmetries is
plausible but either is erroneous or does not match the
most common space group settings (axes and origin). This
is not a problem if I rely on the CIF list but causes a
conflict if I have other phases using the same space group
in the ‘usual’ settings. I can handle this by adding a
character to the group name when the phase originates in
the COD.<o:p></o:p></span></li>
</ol>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Thank you
for your attention, best regards,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal">Pierre Caussin<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<br>
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<pre wrap="" class="moz-quote-pre">_______________________________________________
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</pre>
</blockquote>
<p><br>
</p>
<pre class="moz-signature" cols="72">--
Dr. Saulius Gražulis
Vilnius University Institute of Biotechnology, Saulėtekio al. 7
LT-10257 Vilnius, Lietuva (Lithuania)
mobile: (+370-684)-49802, (+370-614)-36366
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